possible solutions for the problem could be:
- change working directory to z88 binary folder and change back to original working directory before writing the output files
- read config files from a constant path (z88 directory or user directory)
- use a script to copy the binary and config files from z88 folder to working directory and delete the files after calculation is done (you can use this skript like a symbolic link)

For the first two suggestions you have to modify the code and recompile the application. Unfortunately there is no "easy" solution for this problem.